scholarly journals Metagenomic tracking of microbial consortia of cassava flakes (garri)

2021 ◽  
Vol 23 (2) ◽  
pp. 75-82
Author(s):  
B.T. Thomas ◽  
M.O. Efuntoye ◽  
R.M. Kolawole ◽  
O.D. Popoola ◽  
A.O. Tajudeen
Keyword(s):  
Gc Content ◽  
Microbial Consortia ◽  
Metagenomic Data ◽  
Cross Sectional ◽  
Genes Encoding ◽  
Apparent Variation ◽  
Republic Of Benin ◽  
Metagenomic Approach ◽  
Standard Techniques ◽  
Microbial Attack

The affirmation of several cross-sectional studies on the vulnerability of cassava flakes commonly called 'garri' to microbial attack has long been documented. However, longitudinal data on metagenomic tracking of microbial consortia of this important staple food are scarce. Hence, this study was aimed at tracking the microbial consortia of garri. A total of eight samples (four each from both Nigeria and Republic of Benin markets) were randomly collected aseptically using pre-sterilized aluminum pans and processed through a metagenomic approach, while both the chemical and proximate components of garri were assessed following standard techniques. The analysis of the taxonomic consortia of garri reveals the predomination of bacteria (99.82 and 99.81% for samples from Nigeria and Republic of Benin, respectively) while the remaining sequences matched with the Archae (0.07%), fungi (0.09%) and protozoa (0.09%). A large proportion of the sequences were unclassified at the phylum level (approximately 84.10 and 86.2% for Nigerian and Beninese samples, respectively). The reads of cassava flakes metagenome of both Nigeria and Republic of Benin exhibited analogous level of average GC content with sequence count of between 187773-213444 for samples from Nigeria and 157784-198763 for samples from Republic of Benin. The functional characteristics of the inhabiting metagenomes were found containing the genes encoding for adhesins, bacteriocins, resistance to antibiotics, toxic chemicals as well as toxins and superantigens. Both the chemical and the proximate compositions of the examined garri samples, though exhibited significant disparity, but without any apparent variation in the patterns of metagenomic data. Our findings however revealed bacteria as the major contaminants of these cassava food products. Keywords; Metagenomics, Microorganisms, Cassava flakes (garri), Proximate composition

scholarly journals Genetic Variants in Smoking-Related Genes in Two Smoking Cessation Programs: A Cross-Sectional Study

2021 ◽  
Vol 18 (12) ◽  
pp. 6597
Author(s):  
Gloria Pérez-Rubio ◽  
Luis Alberto López-Flores ◽  
Ana Paula Cupertino ◽  
Francisco Cartujano-Barrera ◽  
Luz Myriam Reynales-Shigematsu ◽  
...  
Keyword(s):  
Smoking Cessation ◽  
Cross Sectional Study ◽  
Nucleotide Polymorphisms ◽  
Sectional Study ◽  
Cross Sectional ◽  
Single Nucleotide ◽  
Genotype Frequencies ◽  
Quitting Smoking ◽  
Genes Encoding ◽  
Genomic Regions

Previous studies have identified variants in genes encoding proteins associated with the degree of addiction, smoking onset, and cessation. We aimed to describe thirty-one single nucleotide polymorphisms (SNPs) in seven candidate genomic regions spanning six genes associated with tobacco-smoking in a cross-sectional study from two different interventions for quitting smoking: (1) thirty-eight smokers were recruited via multimedia to participate in e-Decídete! program (e-Dec) and (2) ninety-four attended an institutional smoking cessation program on-site. SNPs genotyping was done by real-time PCR using TaqMan probes. The analysis of alleles and genotypes was carried out using the EpiInfo v7. on-site subjects had more years smoking and tobacco index than e-Dec smokers (p < 0.05, both); in CYP2A6 we found differences in the rs28399433 (p < 0.01), the e-Dec group had a higher frequency of TT genotype (0.78 vs. 0.35), and TG genotype frequency was higher in the on-site group (0.63 vs. 0.18), same as GG genotype (0.03 vs. 0.02). Moreover, three SNPs in NRXN1, two in CHRNA3, and two in CHRNA5 had differences in genotype frequencies (p < 0.01). Cigarettes per day were different (p < 0.05) in the metabolizer classification by CYP2A6 alleles. In conclusion, subjects attending a mobile smoking cessation intervention smoked fewer cigarettes per day, by fewer years, and by fewer cumulative pack-years. There were differences in the genotype frequencies of SNPs in genes related to nicotine metabolism and nicotine dependence. Slow metabolizers smoked more cigarettes per day than intermediate and normal metabolizers.

Formula-fed and Clostridium difficile infected neonatal piglets carry a highly diverse and abundant set of antimicrobial resistance genes

2020 ◽  
Author(s):  
Robert Pieper ◽  
Temesgen Dadi ◽  
Lukasz Grzeskowiak ◽  
Laura Pieper ◽  
Britta Siegmund ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Microbial Colonization ◽  
Metagenomic Data ◽  
Neonatal Piglets ◽  
Gut Colonization ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Genes Encoding

Abstract Background: Clostridium difficile infection (CDI) is an increasing zoonotic health threat and has also been documented as a cause of enteritis outbreaks in neonatal pigs. Furthermore, CDI in neonatal piglets cause changes in microbial gut colonization. We hypothesized that an imbalanced microbial colonization in piglets with CDI could be associated with an altered abundance of antimicrobial resistance genes. Results: We analyzed fecal metagenomic data of lactating sows (S), their piglets during suckling (SP), the same piglets two weeks after weaning (WP), 5-day old artificially reared and formula-fed siblings (FP) and FP infected with C. difficile (FP-CD) for microbiota composition and antimicrobial resistance gene abundance. FP and FP-CD piglets had an immature-type microbiota and increased abundance of antimicrobial resistance genes. A co-occurrence of genes encoding for resistance against aminoglycosides (e.g. aph(3”)-lb, aph(6)-ld, ant(2”)-la), β-lactams (blaCTX-M, blaTEM), fluoroquinolones (pat(A) macrolides (mph(A)), sulfonamides (sul1, sul2), polypeptides (e.g. pmrB, pmrC, arnA, bac(A)) and tetracyclines (e.g. tet(A-D),) was observed. Conclusion: Increased abundance of antimicrobial resistance genes in formula feeding and concomitant CDI may be associated with therapeutic resistance later in life and warrant further studies.

scholarly journals Detection of a Novel, and Likely Ancestral, Tn916-Like Element from a Human Saliva Metagenomic Library

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 548
Author(s):  
Liam J. Reynolds ◽  
Muna F. Anjum ◽  
Adam P. Roberts
Keyword(s):  
Resistance Genes ◽  
Metagenomic Library ◽  
Tetracycline Resistance ◽  
Human Saliva ◽  
Fusion Event ◽  
Tetracycline Resistance Genes ◽  
Antimicrobial Resistance Genes ◽  
Genes Encoding ◽  
Gene Fusion Event ◽  
Metagenomic Approach

Tn916 is a conjugative transposon (CTn) and the first reported and most well characterised of the Tn916/Tn1545 family of CTns. Tn916-like elements have a characteristic modular structure and different members of this family have been identified based on similarities and variations in these modules. In addition to carrying genes encoding proteins required for their conjugation, Tn916-like elements also carry accessory, antimicrobial resistance genes; most commonly the tetracycline resistance gene, tet(M). Our study aimed to identify and characterise tetracycline resistance genes from the human saliva metagenome using a functional metagenomic approach. We identified a tetracycline-resistant clone, TT31, the sequencing of which revealed it to encode both tet(M) and tet(L). Comparison of the TT31 sequence with the accessory, regulation, and recombination modules of other Tn916-like elements indicated that a partial Tn916-like element encoding a truncated orf9 was cloned in TT31. Analysis indicated that a previous insertion within the truncated orf9 created the full length orf9 found in most Tn916-like transposons; demonstrating that orf9 is, in fact, the result of a gene fusion event. Thus, we hypothesise that the Tn916-like element cloned in TT31 likely represents an ancestral Tn916.

scholarly journals Metagenomic Insights into the Effects of Seasonal Temperature Variation on the Activities of Activated Sludge

2019 ◽  
Vol 7 (12) ◽  
pp. 713 ◽  
Author(s):  
Chenbing Ai ◽  
Zhang Yan ◽  
Han Zhou ◽  
Shanshan Hou ◽  
Liyuan Chai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Glutamine Synthetase ◽  
Activated Sludge ◽  
Temperature Variation ◽  
Nitrogen Metabolism ◽  
Metagenomic Data ◽  
Seasonal Temperature ◽  
Simulated Temperature ◽  
Genes Encoding ◽  
Seasonal Temperature Variation

It is well acknowledged that the activities of activated sludge (AS) are influenced by seasonal temperature variation. However, the underlying mechanisms remain largely unknown. Here, the activities of activated sludge under three simulated temperature variation trends were compared in lab-scale. The TN, HN3-H, and COD removal activities of activated sludge were improved as temperature elevated from 20 °C to 35 °C. While, the TN, HN3-H, COD and total phosphorus removal activities of activated sludge were inhibited as temperature declined from 20 °C to 5 °C. Both the extracellular polymer substances (EPS) composition (e.g., total amount, PS, PN and DNA) and sludge index of activated sludge were altered by simulated seasonal temperature variation. The variation of microbial community structures and the functional potentials of activated sludge were further explored by metagenomics. Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes were the dominant phyla for each activated sludge sample under different temperatures. However, the predominant genera of activated sludge were significantly modulated by simulated temperature variation. The functional genes encoding enzymes for nitrogen metabolism in microorganisms were analyzed. The enzyme genes related to ammonification had the highest abundance despite the changing temperature, especially for gene encoding glutamine synthetase. With the temperature raising from 20 °C to 35 °C. The abundance of amoCAB genes encoding ammonia monooxygenase (EC:1.14.99.39) increased by 305.8%. Meanwhile, all the enzyme genes associate with denitrification were reduced. As the temperature declined from 20 °C to 5 °C, the abundance of enzyme genes related to nitrogen metabolism were raised except for carbamate kinase (EC:2.7.2.2), glutamate dehydrogenase (EC:1.4.1.3), glutamine synthetase (EC:6.3.1.2). Metagenomic data indicate that succession of the dominant genera in microbial community structure is, to some extent, beneficial to maintain the functional stability of activated sludge under the temperature variation within a certain temperature range. This study provides novel insights into the effects of seasonal temperature variation on the activities of activated sludge.

Trabeculectomy bleb needling and antimetabolite administration practices in the UK: a glaucoma specialist national survey

2017 ◽  
Vol 102 (9) ◽  
pp. 1244-1247 ◽  
Author(s):  
Karl Mercieca ◽  
Brett Drury ◽  
Archana Bhargava ◽  
Cecilia Fenerty
Keyword(s):  
Online Survey ◽  
Injection Technique ◽  
Cross Sectional ◽  
The United Kingdom ◽  
Treatment Room ◽  
Corneal Toxicity ◽  
Set Up ◽  
The Uk ◽  
Standard Techniques ◽  
Current Practices

AimsTo evaluate, describe and quantify the diversity in postoperative antimetabolite administration and bleb needling practices among glaucoma specialists performing trabeculectomy surgery within the UK and Ireland.MethodsA cross-sectional online survey was distributed to all consultant glaucoma specialists who are on the United Kingdom and Eire Glaucoma Society (UKEGS) contact list. Participants were asked specific questions about their current practices for post-trabeculectomy antimetabolite administration followed by questions directly related to bleb needling procedures.Results60 (83%) of UKEGS glaucoma subspecialty consultants completed the survey. 70% of respondents administered 5-fluorouracil (5-FU) in their clinic room while 30% used a separate treatment room. Doses of 5-FU varied considerably but 70% used 5 mg as standard. Techniques used to reduce corneal toxicity included precipitation with amethocaine (44%) or benoxinate (14%), saline wash (14%) and modified injection technique (8%). Topical antibiotics and/or betadine were used to prevent infection following 5-FU injection in just over 50%. Bleb needling was exclusively performed in operating theatre by 56% of respondents and solely at the slit lamp in the clinic room by 12%. A further 30% used a combination of both theatre and outpatient clinic rooms. Anti-metabolites used were 5-FU (72%) and mitomycin C (22%) with 12% using either of the two substances.ConclusionsThere is a significantly wide variety of current practices for antimetabolite administration and bleb needling within the UK and Ireland. This may be influenced by a glaucoma surgeon’s specific experience and audit results as well as particular clinical set-up, availability of antimetabolite and clinic room space.

scholarly journals Inside environmental Clostridium perfringens genomes: antibiotic resistance genes, virulence factors and genomic features

2020 ◽  
Vol 18 (4) ◽  
pp. 477-493
Author(s):  
Johannes Cornelius Jacobus Fourie ◽  
Cornelius Carlos Bezuidenhout ◽  
Tomasz Janusz Sanko ◽  
Charlotte Mienie ◽  
Rasheed Adeleke
Keyword(s):  
Antibiotic Resistance ◽  
Clostridium Perfringens ◽  
Resistance Genes ◽  
Gc Content ◽  
Antibiotic Resistance Genes ◽  
Open Reading Frames ◽  
Health Security ◽  
Genes Encoding ◽  
Integration Sites ◽  
Potential Pathogenicity

Abstract Until recently, research has focused on Clostridium perfringens in clinical settings without considering environmental isolates. In this study, environmental genomes were used to investigate possible antibiotic resistance and the presence of virulence traits in C. perfringens strains from raw surface water. In silico assembly of three C. perfringens strains, DNA generated almost complete genomes setting their length ranging from 3.4 to 3.6 Mbp with GC content of 28.18%. An average of 3,175 open reading frames was identified, with the majority associated with carbohydrate and protein metabolisms. The genomes harboured several antibiotic resistance genes for glycopeptides, macrolide–lincosamide–streptogramin B, β-lactam, trimethoprim, tetracycline and aminoglycosides and also the presence of several genes encoding for polypeptides and multidrug resistance efflux pumps and 35 virulence genes. Some of these encode for haemolysins, sialidase, hyaluronidase, collagenase, perfringolysin O and phospholipase C. All three genomes contained sequences indicating phage, antibiotic resistance and pathogenic islands integration sites. A genomic comparison of these three strains confirmed high similarity and shared core genes with clinical C. perfringens strains, highlighting their health security risks. This study provides a genomic insight into the potential pathogenicity of C. perfringens present in the environment and emphasises the importance of monitoring this niche in the future.

Polycyclic aromatic hydrocarbon degrading gene islands in five pyrene-degrading Mycobacterium isolates from different geographic locations

2012 ◽  
Vol 58 (1) ◽  
pp. 102-111 ◽  
Author(s):  
Chun Zhang ◽  
Anne J. Anderson
Keyword(s):  
Polycyclic Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbon ◽  
Gc Content ◽  
The United States ◽  
Pcr Analysis ◽  
Transcript Accumulation ◽  
Circular Plasmid ◽  
Genes Encoding ◽  
Polycyclic Aromatic ◽  
Induced Proteins

Mycobacterium sp. strain KMS utilizes pyrene, a high-molecular weight polycyclic aromatic hydrocarbon (PAH), as a sole carbon source. Bioinformatic analysis of the genome of isolate KMS predicted 25 genes with the potential to encode 17 pyrene-induced proteins identified by proteomics; these genes were clustered on both the chromosome and a circular plasmid. RT-PCR analysis of total RNA isolated from KMS cells grown with or without pyrene showed that the presence of pyrene increased the transcript accumulation of 20 of the predicted chromosome- and plasmid-located genes encoding pyrene-induced proteins. The transcribed genes from both the chromosome and a circular plasmid were within larger regions containing genes required for PAH degradation constituting PAH-degrading gene islands. Genes encoding integrases and transposases were found within and outside the PAH-degrading gene islands. The lower GC content of the genes within the gene island (61%–64%) compared with the average genome content (68%) suggested that these mycobacteria initially acquired these genes by horizontal gene transfer. Synteny was detected for the PAH-degrading islands in the genomes of two additional Mycobacterium isolates from the same PAH-polluted site and of two other pyrene-degrading Mycobacterium from different sites in the United States of America. Consequently, the gene islands have been conserved from a common ancestral strain.

scholarly journals Genes encoding intrinsic disorder in Eukaryota have high GC content

2016 ◽  
Vol 4 (1) ◽  
pp. e1262225 ◽  
Author(s):  
Zhenling Peng ◽  
Vladimir N. Uversky ◽  
Lukasz Kurgan
Keyword(s):  
Gc Content ◽  
Intrinsic Disorder ◽  
Genes Encoding

scholarly journals BEEM-Static: Accurate inference of ecological interactions from cross-sectional metagenomic data

2020 ◽  
Author(s):  
Chenhao Li ◽  
Tamar V. Av-Shalom ◽  
Jun Wei Gerald Tan ◽  
Junmei Samantha Kwah ◽  
Kern Rei Chng ◽  
...  
Keyword(s):  
Ecological Model ◽  
Expectation Maximization Algorithm ◽  
Microbial Interactions ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Ecological Interactions ◽  
Cross Sectional ◽  
Key Species ◽  
Alternate Model ◽  
And Function

AbstractMotivationThe structure and function of diverse microbial communities is underpinned by ecological interactions that remain uncharacterized. With rapid adoption of metagenomic sequencing for studying microbiomes, data-driven inference of microbial interactions based on abundance correlations is widely used, but with the drawback that ecological interpretations may not be possible. Leveraging cross-sectional metagenomic datasets for unravelling ecological structure in a scalable manner thus remains an open problem.MethodsWe present an expectation-maximization algorithm (BEEM-Static) that can be applied to cross-sectional datasets to infer interaction networks based on an ecological model (generalized Lotka-Volterra). The method exhibits robustness to violations in model assumptions by using statistical filters to identify and remove corresponding samples.ResultsBenchmarking against 10 state-of-the-art correlation based methods showed that BEEM-Static can infer presence and directionality of ecological interactions even with relative abundance data (AUC-ROC>0.85), a task that other methods struggle with (AUC-ROC<0.63). In addition, BEEM-Static can tolerate a high fraction of samples (up to 40%) being not at steady state or coming from an alternate model. Applying BEEM-Static to a large public dataset of human gut microbiomes (n=4,617) identified multiple stable equilibria that better reflect ecological enterotypes with distinct carrying capacities and interactions for key species.ConclusionBEEM-Static provides new opportunities for mining ecologically interpretable interactions and systems insights from the growing corpus of metagenomic data.

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